Multiple sequence alignment - TraesCS2A01G011500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G011500 chr2A 100.000 3257 0 0 1 3257 4294804 4291548 0.000000e+00 6015.0
1 TraesCS2A01G011500 chr2A 82.650 1268 202 14 996 2257 749104610 749103355 0.000000e+00 1107.0
2 TraesCS2A01G011500 chr2D 94.273 2008 67 19 780 2765 5747372 5749353 0.000000e+00 3027.0
3 TraesCS2A01G011500 chr2D 82.808 1268 200 14 996 2257 618288595 618287340 0.000000e+00 1118.0
4 TraesCS2A01G011500 chr2D 85.772 492 17 15 2779 3245 5749410 5749873 3.800000e-129 472.0
5 TraesCS2A01G011500 chr2D 88.710 62 7 0 155 216 229472878 229472817 3.480000e-10 76.8
6 TraesCS2A01G011500 chr2B 91.302 2035 111 32 780 2772 5628128 5630138 0.000000e+00 2717.0
7 TraesCS2A01G011500 chr2B 82.106 1263 212 11 999 2257 754928667 754927415 0.000000e+00 1068.0
8 TraesCS2A01G011500 chr2B 86.641 524 27 21 2744 3257 5630197 5630687 1.030000e-149 540.0
9 TraesCS2A01G011500 chr2B 81.520 487 38 29 218 690 5627494 5627942 1.440000e-93 353.0
10 TraesCS2A01G011500 chr2B 94.643 56 2 1 155 210 568270367 568270313 5.790000e-13 86.1
11 TraesCS2A01G011500 chr5D 79.375 640 113 16 1044 1672 560433303 560432672 1.790000e-117 433.0
12 TraesCS2A01G011500 chr4A 79.444 647 106 21 1044 1672 603981896 603981259 1.790000e-117 433.0
13 TraesCS2A01G011500 chr4A 91.071 112 5 3 2512 2623 656045843 656045737 2.620000e-31 147.0
14 TraesCS2A01G011500 chr5B 78.783 641 115 19 1044 1672 710786611 710785980 8.410000e-111 411.0
15 TraesCS2A01G011500 chr7A 91.803 61 5 0 155 215 611794078 611794018 5.790000e-13 86.1
16 TraesCS2A01G011500 chr7A 88.406 69 8 0 147 215 684935958 684936026 2.080000e-12 84.2
17 TraesCS2A01G011500 chr3B 91.525 59 5 0 157 215 749866580 749866638 7.490000e-12 82.4
18 TraesCS2A01G011500 chr6B 88.235 68 6 2 162 228 275933648 275933582 2.690000e-11 80.5
19 TraesCS2A01G011500 chr6B 87.302 63 6 2 148 210 47843757 47843817 1.620000e-08 71.3
20 TraesCS2A01G011500 chr1D 88.525 61 5 2 40 100 189656049 189656107 4.510000e-09 73.1
21 TraesCS2A01G011500 chr1D 82.716 81 12 2 137 216 14971023 14970944 1.620000e-08 71.3
22 TraesCS2A01G011500 chr1D 86.154 65 9 0 148 212 101583609 101583673 1.620000e-08 71.3
23 TraesCS2A01G011500 chr1B 88.525 61 5 2 40 100 263552904 263552962 4.510000e-09 73.1
24 TraesCS2A01G011500 chr1A 85.246 61 7 2 40 100 221702940 221702998 9.760000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G011500 chr2A 4291548 4294804 3256 True 6015.000000 6015 100.000000 1 3257 1 chr2A.!!$R1 3256
1 TraesCS2A01G011500 chr2A 749103355 749104610 1255 True 1107.000000 1107 82.650000 996 2257 1 chr2A.!!$R2 1261
2 TraesCS2A01G011500 chr2D 5747372 5749873 2501 False 1749.500000 3027 90.022500 780 3245 2 chr2D.!!$F1 2465
3 TraesCS2A01G011500 chr2D 618287340 618288595 1255 True 1118.000000 1118 82.808000 996 2257 1 chr2D.!!$R2 1261
4 TraesCS2A01G011500 chr2B 5627494 5630687 3193 False 1203.333333 2717 86.487667 218 3257 3 chr2B.!!$F1 3039
5 TraesCS2A01G011500 chr2B 754927415 754928667 1252 True 1068.000000 1068 82.106000 999 2257 1 chr2B.!!$R2 1258
6 TraesCS2A01G011500 chr5D 560432672 560433303 631 True 433.000000 433 79.375000 1044 1672 1 chr5D.!!$R1 628
7 TraesCS2A01G011500 chr4A 603981259 603981896 637 True 433.000000 433 79.444000 1044 1672 1 chr4A.!!$R1 628
8 TraesCS2A01G011500 chr5B 710785980 710786611 631 True 411.000000 411 78.783000 1044 1672 1 chr5B.!!$R1 628

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
207 208 0.038166 TCACCAGCCCATCAAGGTTC 59.962 55.0 0.0 0.0 34.66 3.62 F
208 209 0.251297 CACCAGCCCATCAAGGTTCA 60.251 55.0 0.0 0.0 34.66 3.18 F
258 259 0.257039 GAGGCCCCACTTGTCATCAT 59.743 55.0 0.0 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1689 0.240145 CGGACTTGTACTCGCTGACA 59.760 55.000 0.00 0.0 0.00 3.58 R
1911 2085 1.052124 TCTTGGTGAACCGGGACACT 61.052 55.000 24.68 0.0 39.43 3.55 R
2295 2470 2.547990 AGGGGATTTGGTTAGTCGTCT 58.452 47.619 0.00 0.0 0.00 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.286170 AGAAAGAGTTCATTCTAGTTTTTACCC 57.714 33.333 0.00 0.00 32.81 3.69
33 34 9.286170 GAAAGAGTTCATTCTAGTTTTTACCCT 57.714 33.333 0.00 0.00 33.61 4.34
34 35 9.642343 AAAGAGTTCATTCTAGTTTTTACCCTT 57.358 29.630 0.00 0.00 0.00 3.95
55 56 9.423964 ACCCTTATTAAAGTTTTAGGTTTGTGA 57.576 29.630 0.00 0.00 0.00 3.58
56 57 9.687210 CCCTTATTAAAGTTTTAGGTTTGTGAC 57.313 33.333 0.00 0.00 0.00 3.67
65 66 9.797556 AAGTTTTAGGTTTGTGACAGATTTTAC 57.202 29.630 0.00 0.00 0.00 2.01
66 67 8.410912 AGTTTTAGGTTTGTGACAGATTTTACC 58.589 33.333 0.00 0.00 0.00 2.85
67 68 6.887626 TTAGGTTTGTGACAGATTTTACCC 57.112 37.500 0.00 0.00 0.00 3.69
68 69 4.149598 AGGTTTGTGACAGATTTTACCCC 58.850 43.478 0.00 0.00 0.00 4.95
69 70 3.892588 GGTTTGTGACAGATTTTACCCCA 59.107 43.478 0.00 0.00 0.00 4.96
70 71 4.526650 GGTTTGTGACAGATTTTACCCCAT 59.473 41.667 0.00 0.00 0.00 4.00
71 72 5.011635 GGTTTGTGACAGATTTTACCCCATT 59.988 40.000 0.00 0.00 0.00 3.16
72 73 6.463755 GGTTTGTGACAGATTTTACCCCATTT 60.464 38.462 0.00 0.00 0.00 2.32
73 74 7.256012 GGTTTGTGACAGATTTTACCCCATTTA 60.256 37.037 0.00 0.00 0.00 1.40
74 75 7.461182 TTGTGACAGATTTTACCCCATTTAG 57.539 36.000 0.00 0.00 0.00 1.85
75 76 6.548321 TGTGACAGATTTTACCCCATTTAGT 58.452 36.000 0.00 0.00 0.00 2.24
76 77 7.691213 TGTGACAGATTTTACCCCATTTAGTA 58.309 34.615 0.00 0.00 0.00 1.82
77 78 7.827236 TGTGACAGATTTTACCCCATTTAGTAG 59.173 37.037 0.00 0.00 0.00 2.57
78 79 8.044908 GTGACAGATTTTACCCCATTTAGTAGA 58.955 37.037 0.00 0.00 0.00 2.59
79 80 8.607713 TGACAGATTTTACCCCATTTAGTAGAA 58.392 33.333 0.00 0.00 0.00 2.10
80 81 9.457436 GACAGATTTTACCCCATTTAGTAGAAA 57.543 33.333 0.00 0.00 0.00 2.52
81 82 9.990868 ACAGATTTTACCCCATTTAGTAGAAAT 57.009 29.630 0.00 0.00 0.00 2.17
87 88 9.901172 TTTACCCCATTTAGTAGAAATCTCTTC 57.099 33.333 0.00 0.00 32.70 2.87
88 89 6.901300 ACCCCATTTAGTAGAAATCTCTTCC 58.099 40.000 0.00 0.00 32.70 3.46
89 90 6.447084 ACCCCATTTAGTAGAAATCTCTTCCA 59.553 38.462 0.00 0.00 32.70 3.53
90 91 7.129504 ACCCCATTTAGTAGAAATCTCTTCCAT 59.870 37.037 0.00 0.00 32.70 3.41
91 92 8.001292 CCCCATTTAGTAGAAATCTCTTCCATT 58.999 37.037 0.00 0.00 32.70 3.16
92 93 9.413734 CCCATTTAGTAGAAATCTCTTCCATTT 57.586 33.333 0.00 0.00 32.70 2.32
102 103 9.525826 AGAAATCTCTTCCATTTTACTCAATGT 57.474 29.630 0.00 0.00 32.95 2.71
105 106 7.849804 TCTCTTCCATTTTACTCAATGTAGC 57.150 36.000 0.00 0.00 32.95 3.58
106 107 6.823689 TCTCTTCCATTTTACTCAATGTAGCC 59.176 38.462 0.00 0.00 32.95 3.93
107 108 6.480763 TCTTCCATTTTACTCAATGTAGCCA 58.519 36.000 0.00 0.00 32.95 4.75
108 109 6.945435 TCTTCCATTTTACTCAATGTAGCCAA 59.055 34.615 0.00 0.00 32.95 4.52
109 110 6.509418 TCCATTTTACTCAATGTAGCCAAC 57.491 37.500 0.00 0.00 32.95 3.77
110 111 6.245408 TCCATTTTACTCAATGTAGCCAACT 58.755 36.000 0.00 0.00 32.95 3.16
111 112 6.150976 TCCATTTTACTCAATGTAGCCAACTG 59.849 38.462 0.00 0.00 32.95 3.16
112 113 5.371115 TTTTACTCAATGTAGCCAACTGC 57.629 39.130 0.00 0.00 41.71 4.40
113 114 9.184403 CCATTTTACTCAATGTAGCCAACTGCT 62.184 40.741 0.00 0.00 41.13 4.24
125 126 4.568152 GCCAACTGCTCTCACTTTTAAA 57.432 40.909 0.00 0.00 36.87 1.52
126 127 4.540824 GCCAACTGCTCTCACTTTTAAAG 58.459 43.478 2.81 2.81 36.87 1.85
127 128 4.540824 CCAACTGCTCTCACTTTTAAAGC 58.459 43.478 4.42 0.00 0.00 3.51
128 129 4.540824 CAACTGCTCTCACTTTTAAAGCC 58.459 43.478 4.42 0.00 31.96 4.35
129 130 4.092116 ACTGCTCTCACTTTTAAAGCCT 57.908 40.909 4.42 0.00 31.96 4.58
130 131 4.464947 ACTGCTCTCACTTTTAAAGCCTT 58.535 39.130 4.42 0.00 31.96 4.35
131 132 4.889995 ACTGCTCTCACTTTTAAAGCCTTT 59.110 37.500 4.42 0.00 31.96 3.11
132 133 5.360999 ACTGCTCTCACTTTTAAAGCCTTTT 59.639 36.000 4.42 0.00 31.96 2.27
133 134 6.127338 ACTGCTCTCACTTTTAAAGCCTTTTT 60.127 34.615 4.42 0.00 31.96 1.94
134 135 7.068226 ACTGCTCTCACTTTTAAAGCCTTTTTA 59.932 33.333 4.42 0.00 31.96 1.52
135 136 7.777095 TGCTCTCACTTTTAAAGCCTTTTTAA 58.223 30.769 4.42 0.00 31.96 1.52
136 137 8.254508 TGCTCTCACTTTTAAAGCCTTTTTAAA 58.745 29.630 4.42 0.00 33.53 1.52
137 138 9.093970 GCTCTCACTTTTAAAGCCTTTTTAAAA 57.906 29.630 4.42 13.67 39.86 1.52
149 150 7.581011 AGCCTTTTTAAAAATATGTTCTGCG 57.419 32.000 13.55 0.00 0.00 5.18
150 151 7.375053 AGCCTTTTTAAAAATATGTTCTGCGA 58.625 30.769 13.55 0.00 0.00 5.10
151 152 7.870445 AGCCTTTTTAAAAATATGTTCTGCGAA 59.130 29.630 13.55 0.00 0.00 4.70
152 153 8.655970 GCCTTTTTAAAAATATGTTCTGCGAAT 58.344 29.630 13.55 0.00 0.00 3.34
158 159 9.575783 TTAAAAATATGTTCTGCGAATTAACCC 57.424 29.630 0.00 0.00 0.00 4.11
159 160 5.418310 AATATGTTCTGCGAATTAACCCG 57.582 39.130 0.00 0.00 0.00 5.28
165 166 1.226184 GCGAATTAACCCGCGGTTG 60.226 57.895 26.12 12.62 46.35 3.77
166 167 1.426223 CGAATTAACCCGCGGTTGG 59.574 57.895 26.12 11.78 46.35 3.77
167 168 1.020333 CGAATTAACCCGCGGTTGGA 61.020 55.000 26.12 7.75 46.35 3.53
168 169 1.385528 GAATTAACCCGCGGTTGGAT 58.614 50.000 26.12 9.93 46.35 3.41
169 170 1.064952 GAATTAACCCGCGGTTGGATG 59.935 52.381 26.12 10.10 46.35 3.51
170 171 0.750182 ATTAACCCGCGGTTGGATGG 60.750 55.000 26.12 9.27 46.35 3.51
171 172 2.127027 TTAACCCGCGGTTGGATGGT 62.127 55.000 26.12 10.02 46.35 3.55
172 173 2.127027 TAACCCGCGGTTGGATGGTT 62.127 55.000 26.12 20.22 46.35 3.67
173 174 2.127027 AACCCGCGGTTGGATGGTTA 62.127 55.000 26.12 0.00 45.07 2.85
174 175 1.817941 CCCGCGGTTGGATGGTTAG 60.818 63.158 26.12 0.00 0.00 2.34
175 176 1.817941 CCGCGGTTGGATGGTTAGG 60.818 63.158 19.50 0.00 0.00 2.69
176 177 1.219664 CGCGGTTGGATGGTTAGGA 59.780 57.895 0.00 0.00 0.00 2.94
177 178 0.810031 CGCGGTTGGATGGTTAGGAG 60.810 60.000 0.00 0.00 0.00 3.69
178 179 0.463833 GCGGTTGGATGGTTAGGAGG 60.464 60.000 0.00 0.00 0.00 4.30
179 180 1.200519 CGGTTGGATGGTTAGGAGGA 58.799 55.000 0.00 0.00 0.00 3.71
180 181 1.768870 CGGTTGGATGGTTAGGAGGAT 59.231 52.381 0.00 0.00 0.00 3.24
181 182 2.969950 CGGTTGGATGGTTAGGAGGATA 59.030 50.000 0.00 0.00 0.00 2.59
182 183 3.006967 CGGTTGGATGGTTAGGAGGATAG 59.993 52.174 0.00 0.00 0.00 2.08
183 184 3.974642 GGTTGGATGGTTAGGAGGATAGT 59.025 47.826 0.00 0.00 0.00 2.12
184 185 4.202367 GGTTGGATGGTTAGGAGGATAGTG 60.202 50.000 0.00 0.00 0.00 2.74
185 186 3.587498 TGGATGGTTAGGAGGATAGTGG 58.413 50.000 0.00 0.00 0.00 4.00
186 187 3.051341 TGGATGGTTAGGAGGATAGTGGT 60.051 47.826 0.00 0.00 0.00 4.16
187 188 4.171243 TGGATGGTTAGGAGGATAGTGGTA 59.829 45.833 0.00 0.00 0.00 3.25
188 189 5.162760 TGGATGGTTAGGAGGATAGTGGTAT 60.163 44.000 0.00 0.00 0.00 2.73
189 190 5.422650 GGATGGTTAGGAGGATAGTGGTATC 59.577 48.000 0.00 0.00 35.19 2.24
190 191 5.412617 TGGTTAGGAGGATAGTGGTATCA 57.587 43.478 0.00 0.00 37.39 2.15
191 192 5.145564 TGGTTAGGAGGATAGTGGTATCAC 58.854 45.833 0.00 0.00 43.93 3.06
192 193 4.527427 GGTTAGGAGGATAGTGGTATCACC 59.473 50.000 1.47 0.00 44.64 4.02
201 202 3.019816 TGGTATCACCAGCCCATCA 57.980 52.632 0.00 0.00 44.79 3.07
202 203 1.294041 TGGTATCACCAGCCCATCAA 58.706 50.000 0.00 0.00 44.79 2.57
203 204 1.212688 TGGTATCACCAGCCCATCAAG 59.787 52.381 0.00 0.00 44.79 3.02
204 205 1.477558 GGTATCACCAGCCCATCAAGG 60.478 57.143 0.00 0.00 38.42 3.61
205 206 1.212935 GTATCACCAGCCCATCAAGGT 59.787 52.381 0.00 0.00 34.66 3.50
206 207 0.706433 ATCACCAGCCCATCAAGGTT 59.294 50.000 0.00 0.00 34.66 3.50
207 208 0.038166 TCACCAGCCCATCAAGGTTC 59.962 55.000 0.00 0.00 34.66 3.62
208 209 0.251297 CACCAGCCCATCAAGGTTCA 60.251 55.000 0.00 0.00 34.66 3.18
209 210 0.482446 ACCAGCCCATCAAGGTTCAA 59.518 50.000 0.00 0.00 34.66 2.69
210 211 1.180029 CCAGCCCATCAAGGTTCAAG 58.820 55.000 0.00 0.00 34.66 3.02
211 212 1.548582 CCAGCCCATCAAGGTTCAAGT 60.549 52.381 0.00 0.00 34.66 3.16
212 213 1.815003 CAGCCCATCAAGGTTCAAGTC 59.185 52.381 0.00 0.00 34.66 3.01
213 214 1.177401 GCCCATCAAGGTTCAAGTCC 58.823 55.000 0.00 0.00 34.66 3.85
214 215 1.272147 GCCCATCAAGGTTCAAGTCCT 60.272 52.381 0.00 0.00 36.81 3.85
215 216 2.440409 CCCATCAAGGTTCAAGTCCTG 58.560 52.381 0.00 0.00 35.27 3.86
216 217 2.040278 CCCATCAAGGTTCAAGTCCTGA 59.960 50.000 0.00 0.00 35.27 3.86
222 223 4.103153 TCAAGGTTCAAGTCCTGATCAGTT 59.897 41.667 21.11 6.60 35.27 3.16
235 236 4.218417 CCTGATCAGTTCATTCCGGTTTTT 59.782 41.667 21.11 0.00 32.72 1.94
236 237 5.119931 TGATCAGTTCATTCCGGTTTTTG 57.880 39.130 0.00 0.00 0.00 2.44
257 258 1.685224 GAGGCCCCACTTGTCATCA 59.315 57.895 0.00 0.00 0.00 3.07
258 259 0.257039 GAGGCCCCACTTGTCATCAT 59.743 55.000 0.00 0.00 0.00 2.45
259 260 0.257039 AGGCCCCACTTGTCATCATC 59.743 55.000 0.00 0.00 0.00 2.92
269 270 1.126488 TGTCATCATCCTCCTCTGCC 58.874 55.000 0.00 0.00 0.00 4.85
272 273 2.515071 ATCATCCTCCTCTGCCGCC 61.515 63.158 0.00 0.00 0.00 6.13
306 314 5.670485 AGATGGCAGTCGTAATTAATGACA 58.330 37.500 16.96 9.50 45.20 3.58
309 317 5.483811 TGGCAGTCGTAATTAATGACAAGA 58.516 37.500 16.96 0.00 45.20 3.02
310 318 5.350365 TGGCAGTCGTAATTAATGACAAGAC 59.650 40.000 16.96 12.76 45.20 3.01
313 321 7.277098 GGCAGTCGTAATTAATGACAAGACTAA 59.723 37.037 16.96 0.00 45.20 2.24
324 332 4.585879 TGACAAGACTAATTAACCCTGGC 58.414 43.478 0.00 0.00 0.00 4.85
329 337 1.910671 ACTAATTAACCCTGGCCGTCA 59.089 47.619 0.00 0.00 0.00 4.35
333 341 3.673956 TAACCCTGGCCGTCATGCG 62.674 63.158 0.00 3.02 40.95 4.73
364 372 6.460261 GCTTTCCCTTAATTGACCAGATTAGC 60.460 42.308 0.00 0.00 0.00 3.09
367 375 4.386312 CCCTTAATTGACCAGATTAGCCCA 60.386 45.833 0.00 0.00 0.00 5.36
372 380 3.777106 TGACCAGATTAGCCCATGATC 57.223 47.619 0.00 0.00 0.00 2.92
373 381 2.037641 TGACCAGATTAGCCCATGATCG 59.962 50.000 0.00 0.00 0.00 3.69
376 384 2.617276 CCAGATTAGCCCATGATCGCAT 60.617 50.000 0.00 0.00 34.29 4.73
407 419 0.808847 GCACAGATCTCGATGCAGCA 60.809 55.000 15.19 0.00 38.00 4.41
500 522 3.373565 CTGGAAACAAGGGGCCGC 61.374 66.667 12.88 12.88 42.06 6.53
528 550 2.893895 CGCTCATGCCGTGCTGAT 60.894 61.111 0.00 0.00 35.36 2.90
529 551 2.713770 GCTCATGCCGTGCTGATG 59.286 61.111 0.00 0.00 0.00 3.07
530 552 2.831366 GCTCATGCCGTGCTGATGG 61.831 63.158 0.00 0.00 0.00 3.51
578 600 1.386533 CATCCCTGCATGTGTTCTCC 58.613 55.000 0.00 0.00 0.00 3.71
579 601 1.064906 CATCCCTGCATGTGTTCTCCT 60.065 52.381 0.00 0.00 0.00 3.69
580 602 0.615331 TCCCTGCATGTGTTCTCCTC 59.385 55.000 0.00 0.00 0.00 3.71
581 603 0.325933 CCCTGCATGTGTTCTCCTCA 59.674 55.000 0.00 0.00 0.00 3.86
582 604 1.446907 CCTGCATGTGTTCTCCTCAC 58.553 55.000 0.00 0.00 36.48 3.51
583 605 1.002888 CCTGCATGTGTTCTCCTCACT 59.997 52.381 0.00 0.00 36.83 3.41
606 628 1.675641 ACCCGCCAGAATCTTGCAC 60.676 57.895 7.12 0.00 0.00 4.57
629 651 1.826921 CATGCCATGCACTCCCCTC 60.827 63.158 0.00 0.00 43.04 4.30
630 652 2.005266 ATGCCATGCACTCCCCTCT 61.005 57.895 0.00 0.00 43.04 3.69
634 656 1.694133 CCATGCACTCCCCTCTCTCC 61.694 65.000 0.00 0.00 0.00 3.71
635 657 0.690411 CATGCACTCCCCTCTCTCCT 60.690 60.000 0.00 0.00 0.00 3.69
648 671 3.580458 CCTCTCTCCTCTCTCTCTCTAGG 59.420 56.522 0.00 0.00 0.00 3.02
690 713 9.658799 AAATCAAACTCGAATTTCTCTCTCATA 57.341 29.630 0.00 0.00 0.00 2.15
691 714 9.829507 AATCAAACTCGAATTTCTCTCTCATAT 57.170 29.630 0.00 0.00 0.00 1.78
692 715 9.829507 ATCAAACTCGAATTTCTCTCTCATATT 57.170 29.630 0.00 0.00 0.00 1.28
694 717 9.913451 CAAACTCGAATTTCTCTCTCATATTTC 57.087 33.333 0.00 0.00 0.00 2.17
752 808 5.006261 GCGTTTTTGAAAAATGGCACTTAGT 59.994 36.000 20.41 0.00 0.00 2.24
755 836 5.982465 TTTGAAAAATGGCACTTAGTTGC 57.018 34.783 0.00 0.00 42.18 4.17
758 839 4.340666 TGAAAAATGGCACTTAGTTGCTCA 59.659 37.500 0.00 4.52 42.56 4.26
772 853 0.835276 TGCTCACTCCCTCCATGATG 59.165 55.000 0.00 0.00 0.00 3.07
773 854 1.126488 GCTCACTCCCTCCATGATGA 58.874 55.000 0.00 0.00 0.00 2.92
775 856 2.106166 GCTCACTCCCTCCATGATGATT 59.894 50.000 0.00 0.00 0.00 2.57
776 857 3.806507 GCTCACTCCCTCCATGATGATTC 60.807 52.174 0.00 0.00 0.00 2.52
778 859 2.440627 CACTCCCTCCATGATGATTCCA 59.559 50.000 0.00 0.00 0.00 3.53
779 860 3.074094 CACTCCCTCCATGATGATTCCAT 59.926 47.826 0.00 0.00 35.29 3.41
790 871 4.970860 GATGATTCCATCTCCCTCTTGA 57.029 45.455 0.00 0.00 44.42 3.02
791 872 4.640364 GATGATTCCATCTCCCTCTTGAC 58.360 47.826 0.00 0.00 44.42 3.18
792 873 3.453868 TGATTCCATCTCCCTCTTGACA 58.546 45.455 0.00 0.00 0.00 3.58
793 874 3.198635 TGATTCCATCTCCCTCTTGACAC 59.801 47.826 0.00 0.00 0.00 3.67
794 875 1.573108 TCCATCTCCCTCTTGACACC 58.427 55.000 0.00 0.00 0.00 4.16
795 876 1.079490 TCCATCTCCCTCTTGACACCT 59.921 52.381 0.00 0.00 0.00 4.00
812 932 2.127708 ACCTCCTCCTCTCTCTCTCTC 58.872 57.143 0.00 0.00 0.00 3.20
813 933 2.293856 ACCTCCTCCTCTCTCTCTCTCT 60.294 54.545 0.00 0.00 0.00 3.10
820 950 2.412591 CTCTCTCTCTCTCTCCCTCCT 58.587 57.143 0.00 0.00 0.00 3.69
895 1025 3.510719 ACACATCAGCAACAACAACAAC 58.489 40.909 0.00 0.00 0.00 3.32
896 1026 3.056962 ACACATCAGCAACAACAACAACA 60.057 39.130 0.00 0.00 0.00 3.33
897 1027 3.548668 CACATCAGCAACAACAACAACAG 59.451 43.478 0.00 0.00 0.00 3.16
898 1028 2.276472 TCAGCAACAACAACAACAGC 57.724 45.000 0.00 0.00 0.00 4.40
899 1029 1.135141 TCAGCAACAACAACAACAGCC 60.135 47.619 0.00 0.00 0.00 4.85
900 1030 0.894141 AGCAACAACAACAACAGCCA 59.106 45.000 0.00 0.00 0.00 4.75
901 1031 0.998669 GCAACAACAACAACAGCCAC 59.001 50.000 0.00 0.00 0.00 5.01
902 1032 1.671261 GCAACAACAACAACAGCCACA 60.671 47.619 0.00 0.00 0.00 4.17
903 1033 2.681706 CAACAACAACAACAGCCACAA 58.318 42.857 0.00 0.00 0.00 3.33
911 1041 2.837883 AACAGCCACAACAGCAGCG 61.838 57.895 0.00 0.00 0.00 5.18
934 1066 3.119137 GCAACAAACACCTTCTTCAACCT 60.119 43.478 0.00 0.00 0.00 3.50
935 1067 4.672409 CAACAAACACCTTCTTCAACCTC 58.328 43.478 0.00 0.00 0.00 3.85
936 1068 2.943033 ACAAACACCTTCTTCAACCTCG 59.057 45.455 0.00 0.00 0.00 4.63
937 1069 3.202906 CAAACACCTTCTTCAACCTCGA 58.797 45.455 0.00 0.00 0.00 4.04
1012 1159 2.677289 CCAGCCATGGTGCTCCTCT 61.677 63.158 14.67 0.00 42.17 3.69
1161 1317 2.107953 GAGGACTGCATCGCCTCC 59.892 66.667 15.22 3.26 41.84 4.30
1765 1939 1.203300 TCATGGTGTTCCTCTCCTGGA 60.203 52.381 0.00 0.00 34.23 3.86
2354 2544 5.857394 TGATGAAGATGTTGATTTCGTTCG 58.143 37.500 0.00 0.00 0.00 3.95
2371 2561 6.785488 TCGTTCGTTGTAAGAGTAAGAGTA 57.215 37.500 0.00 0.00 0.00 2.59
2375 2565 7.478044 CGTTCGTTGTAAGAGTAAGAGTAAGAG 59.522 40.741 0.00 0.00 0.00 2.85
2376 2566 7.976135 TCGTTGTAAGAGTAAGAGTAAGAGT 57.024 36.000 0.00 0.00 0.00 3.24
2637 2832 6.073819 GGCTCATTTGACCATGTTGTAAAAAC 60.074 38.462 0.00 0.00 0.00 2.43
2643 2838 5.897050 TGACCATGTTGTAAAAACACCTTC 58.103 37.500 0.00 0.00 32.37 3.46
2688 2890 3.026707 ACTGCCTTTTGTGTAACCCTT 57.973 42.857 0.00 0.00 34.36 3.95
2701 2903 5.176592 GTGTAACCCTTCCTCAGTGAATAC 58.823 45.833 0.00 0.00 0.00 1.89
2767 2973 7.973944 ACAATTTACAGTCTCTTTTTCACCAAC 59.026 33.333 0.00 0.00 0.00 3.77
2772 2978 7.639113 ACAGTCTCTTTTTCACCAACAATTA 57.361 32.000 0.00 0.00 0.00 1.40
2774 2980 8.137437 ACAGTCTCTTTTTCACCAACAATTATG 58.863 33.333 0.00 0.00 0.00 1.90
2775 2981 8.137437 CAGTCTCTTTTTCACCAACAATTATGT 58.863 33.333 0.00 0.00 43.14 2.29
2835 3126 3.068590 CAGCTCCTTCTCATTCTCTCTCC 59.931 52.174 0.00 0.00 0.00 3.71
2851 3142 3.136443 TCTCTCCAGATCTCAGTCTCTCC 59.864 52.174 0.00 0.00 0.00 3.71
2887 3203 7.087639 GGTTACTAGTAGCATTAGCATCTGAG 58.912 42.308 17.27 0.00 45.49 3.35
3022 3346 1.004044 CCTTTGGCTGTCTGACTGGAT 59.996 52.381 15.19 0.00 0.00 3.41
3023 3347 2.354259 CTTTGGCTGTCTGACTGGATC 58.646 52.381 15.19 0.58 0.00 3.36
3024 3348 1.649321 TTGGCTGTCTGACTGGATCT 58.351 50.000 15.19 0.00 0.00 2.75
3025 3349 0.900421 TGGCTGTCTGACTGGATCTG 59.100 55.000 15.19 0.00 0.00 2.90
3026 3350 0.177604 GGCTGTCTGACTGGATCTGG 59.822 60.000 15.19 0.00 0.00 3.86
3027 3351 0.461693 GCTGTCTGACTGGATCTGGC 60.462 60.000 15.19 0.00 0.00 4.85
3028 3352 1.193323 CTGTCTGACTGGATCTGGCT 58.807 55.000 9.51 0.00 32.34 4.75
3054 3378 4.360643 TGGCCATCCCAATTGCTC 57.639 55.556 0.00 0.00 41.82 4.26
3055 3379 1.699137 TGGCCATCCCAATTGCTCT 59.301 52.632 0.00 0.00 41.82 4.09
3056 3380 0.685131 TGGCCATCCCAATTGCTCTG 60.685 55.000 0.00 0.00 41.82 3.35
3057 3381 1.397390 GGCCATCCCAATTGCTCTGG 61.397 60.000 0.00 6.95 0.00 3.86
3058 3382 2.024590 GCCATCCCAATTGCTCTGGC 62.025 60.000 20.51 20.51 42.00 4.85
3059 3383 0.396695 CCATCCCAATTGCTCTGGCT 60.397 55.000 0.00 0.00 39.59 4.75
3060 3384 0.744874 CATCCCAATTGCTCTGGCTG 59.255 55.000 0.00 0.00 39.59 4.85
3061 3385 0.396695 ATCCCAATTGCTCTGGCTGG 60.397 55.000 0.00 0.00 39.59 4.85
3115 3448 3.168035 ACCAGATCTCACTCACTCACT 57.832 47.619 0.00 0.00 0.00 3.41
3118 3451 3.119531 CCAGATCTCACTCACTCACTCAC 60.120 52.174 0.00 0.00 0.00 3.51
3128 3461 0.470833 ACTCACTCACTCACCCTGCT 60.471 55.000 0.00 0.00 0.00 4.24
3173 3508 2.360852 CCACCTGCTGCCTCCAAG 60.361 66.667 0.00 0.00 0.00 3.61
3174 3509 2.360852 CACCTGCTGCCTCCAAGG 60.361 66.667 0.00 0.00 38.80 3.61
3175 3510 2.856000 ACCTGCTGCCTCCAAGGT 60.856 61.111 3.00 3.00 37.80 3.50
3176 3511 2.360852 CCTGCTGCCTCCAAGGTG 60.361 66.667 0.00 0.00 37.80 4.00
3177 3512 2.360852 CTGCTGCCTCCAAGGTGG 60.361 66.667 2.83 2.83 37.80 4.61
3178 3513 3.177884 TGCTGCCTCCAAGGTGGT 61.178 61.111 8.83 0.00 39.03 4.16
3214 3549 1.004044 CTGCCAAGATTCCACCAGTCT 59.996 52.381 0.00 0.00 0.00 3.24
3245 3581 7.362920 CCCCCAAAGTCAATCACTAAACTAATG 60.363 40.741 0.00 0.00 32.30 1.90
3250 3586 7.617041 AGTCAATCACTAAACTAATGCCTTC 57.383 36.000 0.00 0.00 31.37 3.46
3253 3589 8.462016 GTCAATCACTAAACTAATGCCTTCATT 58.538 33.333 0.00 0.00 44.52 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.286170 GGGTAAAAACTAGAATGAACTCTTTCT 57.714 33.333 11.34 11.34 41.40 2.52
7 8 9.286170 AGGGTAAAAACTAGAATGAACTCTTTC 57.714 33.333 0.00 0.00 0.00 2.62
8 9 9.642343 AAGGGTAAAAACTAGAATGAACTCTTT 57.358 29.630 0.00 0.00 0.00 2.52
29 30 9.423964 TCACAAACCTAAAACTTTAATAAGGGT 57.576 29.630 0.00 0.00 35.61 4.34
30 31 9.687210 GTCACAAACCTAAAACTTTAATAAGGG 57.313 33.333 0.00 0.00 35.61 3.95
39 40 9.797556 GTAAAATCTGTCACAAACCTAAAACTT 57.202 29.630 0.00 0.00 0.00 2.66
40 41 8.410912 GGTAAAATCTGTCACAAACCTAAAACT 58.589 33.333 0.00 0.00 0.00 2.66
41 42 7.650504 GGGTAAAATCTGTCACAAACCTAAAAC 59.349 37.037 0.00 0.00 0.00 2.43
42 43 7.201929 GGGGTAAAATCTGTCACAAACCTAAAA 60.202 37.037 0.00 0.00 0.00 1.52
43 44 6.265876 GGGGTAAAATCTGTCACAAACCTAAA 59.734 38.462 0.00 0.00 0.00 1.85
44 45 5.771165 GGGGTAAAATCTGTCACAAACCTAA 59.229 40.000 0.00 0.00 0.00 2.69
45 46 5.163077 TGGGGTAAAATCTGTCACAAACCTA 60.163 40.000 0.00 0.00 0.00 3.08
46 47 4.149598 GGGGTAAAATCTGTCACAAACCT 58.850 43.478 0.00 0.00 0.00 3.50
47 48 3.892588 TGGGGTAAAATCTGTCACAAACC 59.107 43.478 0.00 0.00 0.00 3.27
48 49 5.722021 ATGGGGTAAAATCTGTCACAAAC 57.278 39.130 0.00 0.00 0.00 2.93
49 50 6.739331 AAATGGGGTAAAATCTGTCACAAA 57.261 33.333 0.00 0.00 0.00 2.83
50 51 7.007723 ACTAAATGGGGTAAAATCTGTCACAA 58.992 34.615 0.00 0.00 0.00 3.33
51 52 6.548321 ACTAAATGGGGTAAAATCTGTCACA 58.452 36.000 0.00 0.00 0.00 3.58
52 53 8.044908 TCTACTAAATGGGGTAAAATCTGTCAC 58.955 37.037 0.00 0.00 0.00 3.67
53 54 8.153221 TCTACTAAATGGGGTAAAATCTGTCA 57.847 34.615 0.00 0.00 0.00 3.58
54 55 9.457436 TTTCTACTAAATGGGGTAAAATCTGTC 57.543 33.333 0.00 0.00 0.00 3.51
55 56 9.990868 ATTTCTACTAAATGGGGTAAAATCTGT 57.009 29.630 0.00 0.00 0.00 3.41
61 62 9.901172 GAAGAGATTTCTACTAAATGGGGTAAA 57.099 33.333 0.00 0.00 31.96 2.01
62 63 8.491958 GGAAGAGATTTCTACTAAATGGGGTAA 58.508 37.037 0.00 0.00 31.96 2.85
63 64 7.626084 TGGAAGAGATTTCTACTAAATGGGGTA 59.374 37.037 0.00 0.00 31.96 3.69
64 65 6.447084 TGGAAGAGATTTCTACTAAATGGGGT 59.553 38.462 0.00 0.00 31.96 4.95
65 66 6.900194 TGGAAGAGATTTCTACTAAATGGGG 58.100 40.000 0.00 0.00 31.96 4.96
66 67 8.986929 AATGGAAGAGATTTCTACTAAATGGG 57.013 34.615 0.00 0.00 31.96 4.00
76 77 9.525826 ACATTGAGTAAAATGGAAGAGATTTCT 57.474 29.630 2.34 0.00 41.06 2.52
79 80 8.897752 GCTACATTGAGTAAAATGGAAGAGATT 58.102 33.333 2.34 0.00 41.06 2.40
80 81 7.500559 GGCTACATTGAGTAAAATGGAAGAGAT 59.499 37.037 2.34 0.00 41.06 2.75
81 82 6.823689 GGCTACATTGAGTAAAATGGAAGAGA 59.176 38.462 2.34 0.00 41.06 3.10
82 83 6.599244 TGGCTACATTGAGTAAAATGGAAGAG 59.401 38.462 2.34 0.00 41.06 2.85
83 84 6.480763 TGGCTACATTGAGTAAAATGGAAGA 58.519 36.000 2.34 0.00 41.06 2.87
84 85 6.757897 TGGCTACATTGAGTAAAATGGAAG 57.242 37.500 2.34 1.01 41.06 3.46
85 86 6.719370 AGTTGGCTACATTGAGTAAAATGGAA 59.281 34.615 1.24 0.00 41.06 3.53
86 87 6.150976 CAGTTGGCTACATTGAGTAAAATGGA 59.849 38.462 1.24 0.00 41.06 3.41
87 88 6.324819 CAGTTGGCTACATTGAGTAAAATGG 58.675 40.000 1.24 0.00 41.06 3.16
88 89 5.801947 GCAGTTGGCTACATTGAGTAAAATG 59.198 40.000 1.24 0.00 40.21 2.32
89 90 5.954335 GCAGTTGGCTACATTGAGTAAAAT 58.046 37.500 1.24 0.00 40.25 1.82
90 91 5.371115 GCAGTTGGCTACATTGAGTAAAA 57.629 39.130 1.24 0.00 40.25 1.52
104 105 4.540824 CTTTAAAAGTGAGAGCAGTTGGC 58.459 43.478 0.00 0.00 45.30 4.52
105 106 4.540824 GCTTTAAAAGTGAGAGCAGTTGG 58.459 43.478 0.00 0.00 37.71 3.77
106 107 4.276926 AGGCTTTAAAAGTGAGAGCAGTTG 59.723 41.667 0.00 0.00 37.71 3.16
107 108 4.464947 AGGCTTTAAAAGTGAGAGCAGTT 58.535 39.130 0.00 0.00 39.30 3.16
108 109 4.092116 AGGCTTTAAAAGTGAGAGCAGT 57.908 40.909 0.00 0.00 35.12 4.40
109 110 5.444663 AAAGGCTTTAAAAGTGAGAGCAG 57.555 39.130 11.52 0.00 35.12 4.24
110 111 5.852282 AAAAGGCTTTAAAAGTGAGAGCA 57.148 34.783 13.77 0.00 35.12 4.26
111 112 8.642908 TTTAAAAAGGCTTTAAAAGTGAGAGC 57.357 30.769 13.77 0.00 32.75 4.09
123 124 8.495148 CGCAGAACATATTTTTAAAAAGGCTTT 58.505 29.630 17.72 6.68 0.00 3.51
124 125 7.870445 TCGCAGAACATATTTTTAAAAAGGCTT 59.130 29.630 17.72 0.00 0.00 4.35
125 126 7.375053 TCGCAGAACATATTTTTAAAAAGGCT 58.625 30.769 17.72 5.21 0.00 4.58
126 127 7.575332 TCGCAGAACATATTTTTAAAAAGGC 57.425 32.000 17.72 9.98 0.00 4.35
132 133 9.575783 GGGTTAATTCGCAGAACATATTTTTAA 57.424 29.630 0.00 0.00 45.90 1.52
133 134 7.911205 CGGGTTAATTCGCAGAACATATTTTTA 59.089 33.333 0.00 0.00 45.90 1.52
134 135 6.750039 CGGGTTAATTCGCAGAACATATTTTT 59.250 34.615 0.00 0.00 45.90 1.94
135 136 6.262601 CGGGTTAATTCGCAGAACATATTTT 58.737 36.000 0.00 0.00 45.90 1.82
136 137 5.816919 CGGGTTAATTCGCAGAACATATTT 58.183 37.500 0.00 0.00 45.90 1.40
137 138 5.418310 CGGGTTAATTCGCAGAACATATT 57.582 39.130 0.00 0.00 45.90 1.28
147 148 1.226184 CAACCGCGGGTTAATTCGC 60.226 57.895 31.76 13.15 45.01 4.70
148 149 1.020333 TCCAACCGCGGGTTAATTCG 61.020 55.000 31.76 9.90 45.01 3.34
149 150 1.064952 CATCCAACCGCGGGTTAATTC 59.935 52.381 31.76 0.00 45.01 2.17
150 151 1.099689 CATCCAACCGCGGGTTAATT 58.900 50.000 31.76 11.61 45.01 1.40
151 152 0.750182 CCATCCAACCGCGGGTTAAT 60.750 55.000 31.76 16.05 45.01 1.40
152 153 1.377463 CCATCCAACCGCGGGTTAA 60.377 57.895 31.76 14.14 45.01 2.01
153 154 2.127027 AACCATCCAACCGCGGGTTA 62.127 55.000 31.76 14.59 45.01 2.85
155 156 2.530958 CTAACCATCCAACCGCGGGT 62.531 60.000 31.76 23.68 37.65 5.28
156 157 1.817941 CTAACCATCCAACCGCGGG 60.818 63.158 31.76 12.82 0.00 6.13
157 158 1.817941 CCTAACCATCCAACCGCGG 60.818 63.158 26.86 26.86 0.00 6.46
158 159 0.810031 CTCCTAACCATCCAACCGCG 60.810 60.000 0.00 0.00 0.00 6.46
159 160 0.463833 CCTCCTAACCATCCAACCGC 60.464 60.000 0.00 0.00 0.00 5.68
160 161 1.200519 TCCTCCTAACCATCCAACCG 58.799 55.000 0.00 0.00 0.00 4.44
161 162 3.974642 ACTATCCTCCTAACCATCCAACC 59.025 47.826 0.00 0.00 0.00 3.77
162 163 4.202367 CCACTATCCTCCTAACCATCCAAC 60.202 50.000 0.00 0.00 0.00 3.77
163 164 3.973973 CCACTATCCTCCTAACCATCCAA 59.026 47.826 0.00 0.00 0.00 3.53
164 165 3.051341 ACCACTATCCTCCTAACCATCCA 60.051 47.826 0.00 0.00 0.00 3.41
165 166 3.588569 ACCACTATCCTCCTAACCATCC 58.411 50.000 0.00 0.00 0.00 3.51
166 167 6.017192 TGATACCACTATCCTCCTAACCATC 58.983 44.000 0.00 0.00 0.00 3.51
167 168 5.780793 GTGATACCACTATCCTCCTAACCAT 59.219 44.000 0.00 0.00 40.10 3.55
168 169 5.145564 GTGATACCACTATCCTCCTAACCA 58.854 45.833 0.00 0.00 40.10 3.67
169 170 4.527427 GGTGATACCACTATCCTCCTAACC 59.473 50.000 0.00 0.00 42.77 2.85
170 171 5.145564 TGGTGATACCACTATCCTCCTAAC 58.854 45.833 0.00 0.00 44.79 2.34
171 172 5.394738 CTGGTGATACCACTATCCTCCTAA 58.605 45.833 0.00 0.00 44.79 2.69
172 173 4.753217 GCTGGTGATACCACTATCCTCCTA 60.753 50.000 0.00 0.00 44.79 2.94
173 174 3.850752 CTGGTGATACCACTATCCTCCT 58.149 50.000 0.00 0.00 44.79 3.69
174 175 2.300437 GCTGGTGATACCACTATCCTCC 59.700 54.545 0.00 0.00 44.79 4.30
175 176 2.300437 GGCTGGTGATACCACTATCCTC 59.700 54.545 0.00 0.00 44.79 3.71
176 177 2.330216 GGCTGGTGATACCACTATCCT 58.670 52.381 0.00 0.00 44.79 3.24
177 178 1.348036 GGGCTGGTGATACCACTATCC 59.652 57.143 0.00 0.00 44.79 2.59
178 179 2.047061 TGGGCTGGTGATACCACTATC 58.953 52.381 0.00 0.00 44.79 2.08
179 180 2.190398 TGGGCTGGTGATACCACTAT 57.810 50.000 0.00 0.00 44.79 2.12
180 181 2.047061 GATGGGCTGGTGATACCACTA 58.953 52.381 0.00 0.00 44.79 2.74
181 182 0.839946 GATGGGCTGGTGATACCACT 59.160 55.000 0.00 0.00 44.79 4.00
182 183 0.546122 TGATGGGCTGGTGATACCAC 59.454 55.000 0.00 0.00 44.79 4.16
184 185 1.477558 CCTTGATGGGCTGGTGATACC 60.478 57.143 0.00 0.00 39.22 2.73
185 186 1.212935 ACCTTGATGGGCTGGTGATAC 59.787 52.381 0.00 0.00 41.11 2.24
186 187 1.595311 ACCTTGATGGGCTGGTGATA 58.405 50.000 0.00 0.00 41.11 2.15
187 188 0.706433 AACCTTGATGGGCTGGTGAT 59.294 50.000 0.00 0.00 41.11 3.06
188 189 0.038166 GAACCTTGATGGGCTGGTGA 59.962 55.000 0.00 0.00 41.11 4.02
189 190 0.251297 TGAACCTTGATGGGCTGGTG 60.251 55.000 0.00 0.00 41.11 4.17
190 191 0.482446 TTGAACCTTGATGGGCTGGT 59.518 50.000 0.00 0.00 41.11 4.00
191 192 1.180029 CTTGAACCTTGATGGGCTGG 58.820 55.000 0.00 0.00 41.11 4.85
192 193 1.815003 GACTTGAACCTTGATGGGCTG 59.185 52.381 0.00 0.00 41.11 4.85
193 194 1.272147 GGACTTGAACCTTGATGGGCT 60.272 52.381 0.00 0.00 41.11 5.19
194 195 1.177401 GGACTTGAACCTTGATGGGC 58.823 55.000 0.00 0.00 41.11 5.36
195 196 2.040278 TCAGGACTTGAACCTTGATGGG 59.960 50.000 0.00 0.00 41.11 4.00
196 197 3.423539 TCAGGACTTGAACCTTGATGG 57.576 47.619 0.00 0.00 42.93 3.51
197 198 4.582869 TGATCAGGACTTGAACCTTGATG 58.417 43.478 0.00 0.00 39.77 3.07
198 199 4.288105 ACTGATCAGGACTTGAACCTTGAT 59.712 41.667 26.08 0.00 39.77 2.57
199 200 3.648067 ACTGATCAGGACTTGAACCTTGA 59.352 43.478 26.08 0.00 39.77 3.02
200 201 4.013267 ACTGATCAGGACTTGAACCTTG 57.987 45.455 26.08 0.00 39.77 3.61
201 202 4.103153 TGAACTGATCAGGACTTGAACCTT 59.897 41.667 26.08 7.57 39.77 3.50
202 203 3.648067 TGAACTGATCAGGACTTGAACCT 59.352 43.478 26.08 0.00 39.77 3.50
203 204 4.008074 TGAACTGATCAGGACTTGAACC 57.992 45.455 26.08 5.40 39.77 3.62
204 205 5.123027 GGAATGAACTGATCAGGACTTGAAC 59.877 44.000 26.08 10.23 42.53 3.18
205 206 5.248640 GGAATGAACTGATCAGGACTTGAA 58.751 41.667 26.08 5.46 42.53 2.69
206 207 4.621510 CGGAATGAACTGATCAGGACTTGA 60.622 45.833 26.08 6.90 42.53 3.02
207 208 3.620374 CGGAATGAACTGATCAGGACTTG 59.380 47.826 26.08 1.57 42.53 3.16
208 209 3.369892 CCGGAATGAACTGATCAGGACTT 60.370 47.826 26.08 11.94 42.53 3.01
209 210 2.169352 CCGGAATGAACTGATCAGGACT 59.831 50.000 26.08 10.55 42.53 3.85
210 211 2.093447 ACCGGAATGAACTGATCAGGAC 60.093 50.000 26.08 18.50 42.53 3.85
211 212 2.187958 ACCGGAATGAACTGATCAGGA 58.812 47.619 26.08 10.42 42.53 3.86
212 213 2.698855 ACCGGAATGAACTGATCAGG 57.301 50.000 26.08 8.85 42.53 3.86
213 214 5.156355 CAAAAACCGGAATGAACTGATCAG 58.844 41.667 21.37 21.37 42.53 2.90
214 215 4.582656 ACAAAAACCGGAATGAACTGATCA 59.417 37.500 9.46 0.00 43.67 2.92
215 216 5.121221 ACAAAAACCGGAATGAACTGATC 57.879 39.130 9.46 0.00 0.00 2.92
216 217 4.320202 CGACAAAAACCGGAATGAACTGAT 60.320 41.667 9.46 0.00 0.00 2.90
222 223 2.147958 CCTCGACAAAAACCGGAATGA 58.852 47.619 9.46 0.00 0.00 2.57
235 236 2.847234 ACAAGTGGGGCCTCGACA 60.847 61.111 0.84 0.00 0.00 4.35
236 237 2.047179 GACAAGTGGGGCCTCGAC 60.047 66.667 0.84 0.00 0.00 4.20
269 270 0.819259 CCATCTTACATGTGGGGGCG 60.819 60.000 9.11 0.00 0.00 6.13
272 273 1.064463 ACTGCCATCTTACATGTGGGG 60.064 52.381 9.11 3.78 33.58 4.96
306 314 2.574824 ACGGCCAGGGTTAATTAGTCTT 59.425 45.455 2.24 0.00 0.00 3.01
309 317 1.910671 TGACGGCCAGGGTTAATTAGT 59.089 47.619 2.24 0.00 0.00 2.24
310 318 2.702592 TGACGGCCAGGGTTAATTAG 57.297 50.000 2.24 0.00 0.00 1.73
313 321 0.751643 GCATGACGGCCAGGGTTAAT 60.752 55.000 2.24 0.00 0.00 1.40
329 337 1.252904 AAGGGAAAGCATGCACGCAT 61.253 50.000 21.98 9.21 37.08 4.73
333 341 4.176271 GTCAATTAAGGGAAAGCATGCAC 58.824 43.478 21.98 10.59 0.00 4.57
336 344 4.706476 TCTGGTCAATTAAGGGAAAGCATG 59.294 41.667 0.00 0.00 0.00 4.06
337 345 4.934356 TCTGGTCAATTAAGGGAAAGCAT 58.066 39.130 0.00 0.00 0.00 3.79
338 346 4.380843 TCTGGTCAATTAAGGGAAAGCA 57.619 40.909 0.00 0.00 0.00 3.91
339 347 5.921962 AATCTGGTCAATTAAGGGAAAGC 57.078 39.130 0.00 0.00 0.00 3.51
340 348 6.039829 GGCTAATCTGGTCAATTAAGGGAAAG 59.960 42.308 0.00 0.00 0.00 2.62
343 351 4.141251 GGGCTAATCTGGTCAATTAAGGGA 60.141 45.833 0.00 0.00 0.00 4.20
382 390 1.859703 CATCGAGATCTGTGCTCTTGC 59.140 52.381 0.00 0.00 40.20 4.01
383 391 1.859703 GCATCGAGATCTGTGCTCTTG 59.140 52.381 0.00 0.00 34.85 3.02
385 393 1.067364 CTGCATCGAGATCTGTGCTCT 59.933 52.381 19.29 0.00 38.37 4.09
386 394 1.489574 CTGCATCGAGATCTGTGCTC 58.510 55.000 19.29 0.00 38.37 4.26
387 395 0.530211 GCTGCATCGAGATCTGTGCT 60.530 55.000 19.29 0.00 38.37 4.40
422 434 4.640113 CGCGCGCTTATCTGCAGC 62.640 66.667 30.48 0.00 34.48 5.25
423 435 3.993234 CCGCGCGCTTATCTGCAG 61.993 66.667 30.48 7.63 0.00 4.41
456 468 2.505405 GGAGTTGAAGAAGGTTGGACC 58.495 52.381 0.00 0.00 38.99 4.46
457 469 2.505405 GGGAGTTGAAGAAGGTTGGAC 58.495 52.381 0.00 0.00 0.00 4.02
458 470 1.423921 GGGGAGTTGAAGAAGGTTGGA 59.576 52.381 0.00 0.00 0.00 3.53
459 471 1.547901 GGGGGAGTTGAAGAAGGTTGG 60.548 57.143 0.00 0.00 0.00 3.77
460 472 1.882352 CGGGGGAGTTGAAGAAGGTTG 60.882 57.143 0.00 0.00 0.00 3.77
461 473 0.400594 CGGGGGAGTTGAAGAAGGTT 59.599 55.000 0.00 0.00 0.00 3.50
462 474 0.473117 TCGGGGGAGTTGAAGAAGGT 60.473 55.000 0.00 0.00 0.00 3.50
463 475 0.250513 CTCGGGGGAGTTGAAGAAGG 59.749 60.000 0.00 0.00 0.00 3.46
474 486 2.124507 CTTGTTTCCAGCTCGGGGGA 62.125 60.000 2.86 0.00 34.36 4.81
475 487 1.675641 CTTGTTTCCAGCTCGGGGG 60.676 63.158 2.86 0.00 34.36 5.40
511 533 2.893895 ATCAGCACGGCATGAGCG 60.894 61.111 0.00 0.00 43.41 5.03
513 535 3.417601 CCATCAGCACGGCATGAG 58.582 61.111 0.00 0.00 0.00 2.90
524 546 3.592814 CATGCAGGCGGCCATCAG 61.593 66.667 23.09 9.04 43.89 2.90
525 547 3.942377 AACATGCAGGCGGCCATCA 62.942 57.895 23.09 17.99 43.89 3.07
526 548 3.129913 GAACATGCAGGCGGCCATC 62.130 63.158 23.09 12.56 43.89 3.51
527 549 3.142838 GAACATGCAGGCGGCCAT 61.143 61.111 23.09 2.70 43.89 4.40
528 550 4.349503 AGAACATGCAGGCGGCCA 62.350 61.111 23.09 0.00 43.89 5.36
529 551 3.512516 GAGAACATGCAGGCGGCC 61.513 66.667 12.11 12.11 43.89 6.13
530 552 3.512516 GGAGAACATGCAGGCGGC 61.513 66.667 0.00 0.00 45.13 6.53
531 553 2.046023 TGGAGAACATGCAGGCGG 60.046 61.111 0.00 0.00 0.00 6.13
532 554 2.743752 CGTGGAGAACATGCAGGCG 61.744 63.158 0.00 0.00 0.00 5.52
533 555 2.401766 CCGTGGAGAACATGCAGGC 61.402 63.158 0.00 0.00 34.15 4.85
574 596 1.000771 CGGGTGAGGAGTGAGGAGA 60.001 63.158 0.00 0.00 0.00 3.71
578 600 2.997315 TGGCGGGTGAGGAGTGAG 60.997 66.667 0.00 0.00 0.00 3.51
579 601 2.997315 CTGGCGGGTGAGGAGTGA 60.997 66.667 0.00 0.00 0.00 3.41
580 602 1.903877 ATTCTGGCGGGTGAGGAGTG 61.904 60.000 0.00 0.00 0.00 3.51
581 603 1.613630 ATTCTGGCGGGTGAGGAGT 60.614 57.895 0.00 0.00 0.00 3.85
582 604 1.144936 GATTCTGGCGGGTGAGGAG 59.855 63.158 0.00 0.00 0.00 3.69
583 605 0.909610 AAGATTCTGGCGGGTGAGGA 60.910 55.000 0.00 0.00 0.00 3.71
613 635 2.611800 AGAGGGGAGTGCATGGCA 60.612 61.111 0.00 0.00 35.60 4.92
614 636 2.191641 GAGAGGGGAGTGCATGGC 59.808 66.667 0.00 0.00 0.00 4.40
623 645 1.010793 AGAGAGAGAGGAGAGAGGGGA 59.989 57.143 0.00 0.00 0.00 4.81
629 651 5.630415 TTTCCTAGAGAGAGAGAGGAGAG 57.370 47.826 0.00 0.00 39.25 3.20
630 652 6.395780 TTTTTCCTAGAGAGAGAGAGGAGA 57.604 41.667 0.00 0.00 39.25 3.71
660 683 8.078596 AGAGAGAAATTCGAGTTTGATTTTTGG 58.921 33.333 10.93 0.00 0.00 3.28
667 690 9.658799 AAATATGAGAGAGAAATTCGAGTTTGA 57.341 29.630 10.93 0.00 0.00 2.69
708 764 6.688637 ACGCCAACTTCTTTTTAGTTTAGT 57.311 33.333 0.00 0.00 33.73 2.24
709 765 7.980742 AAACGCCAACTTCTTTTTAGTTTAG 57.019 32.000 0.00 0.00 33.73 1.85
710 766 8.648968 CAAAAACGCCAACTTCTTTTTAGTTTA 58.351 29.630 0.00 0.00 33.73 2.01
711 767 7.385478 TCAAAAACGCCAACTTCTTTTTAGTTT 59.615 29.630 0.00 0.00 33.73 2.66
712 768 6.869388 TCAAAAACGCCAACTTCTTTTTAGTT 59.131 30.769 0.00 0.00 36.31 2.24
713 769 6.391537 TCAAAAACGCCAACTTCTTTTTAGT 58.608 32.000 0.00 0.00 0.00 2.24
714 770 6.879188 TCAAAAACGCCAACTTCTTTTTAG 57.121 33.333 0.00 0.00 0.00 1.85
718 774 6.546972 TTTTTCAAAAACGCCAACTTCTTT 57.453 29.167 0.00 0.00 0.00 2.52
729 785 6.582437 ACTAAGTGCCATTTTTCAAAAACG 57.418 33.333 0.00 0.00 0.00 3.60
752 808 1.211212 CATCATGGAGGGAGTGAGCAA 59.789 52.381 0.00 0.00 0.00 3.91
755 836 3.244491 GGAATCATCATGGAGGGAGTGAG 60.244 52.174 0.00 0.00 0.00 3.51
758 839 2.780414 TGGAATCATCATGGAGGGAGT 58.220 47.619 0.00 0.00 0.00 3.85
772 853 3.432890 GGTGTCAAGAGGGAGATGGAATC 60.433 52.174 0.00 0.00 46.04 2.52
773 854 2.507471 GGTGTCAAGAGGGAGATGGAAT 59.493 50.000 0.00 0.00 0.00 3.01
775 856 1.079490 AGGTGTCAAGAGGGAGATGGA 59.921 52.381 0.00 0.00 0.00 3.41
776 857 1.484240 GAGGTGTCAAGAGGGAGATGG 59.516 57.143 0.00 0.00 0.00 3.51
778 859 1.364328 AGGAGGTGTCAAGAGGGAGAT 59.636 52.381 0.00 0.00 0.00 2.75
779 860 0.787084 AGGAGGTGTCAAGAGGGAGA 59.213 55.000 0.00 0.00 0.00 3.71
780 861 1.190643 GAGGAGGTGTCAAGAGGGAG 58.809 60.000 0.00 0.00 0.00 4.30
781 862 0.252284 GGAGGAGGTGTCAAGAGGGA 60.252 60.000 0.00 0.00 0.00 4.20
783 864 1.190643 GAGGAGGAGGTGTCAAGAGG 58.809 60.000 0.00 0.00 0.00 3.69
788 869 1.283613 GAGAGAGAGGAGGAGGTGTCA 59.716 57.143 0.00 0.00 0.00 3.58
789 870 1.564348 AGAGAGAGAGGAGGAGGTGTC 59.436 57.143 0.00 0.00 0.00 3.67
790 871 1.564348 GAGAGAGAGAGGAGGAGGTGT 59.436 57.143 0.00 0.00 0.00 4.16
791 872 1.846439 AGAGAGAGAGAGGAGGAGGTG 59.154 57.143 0.00 0.00 0.00 4.00
792 873 2.127708 GAGAGAGAGAGAGGAGGAGGT 58.872 57.143 0.00 0.00 0.00 3.85
793 874 2.370189 GAGAGAGAGAGAGAGGAGGAGG 59.630 59.091 0.00 0.00 0.00 4.30
794 875 2.370189 GGAGAGAGAGAGAGAGGAGGAG 59.630 59.091 0.00 0.00 0.00 3.69
795 876 2.408565 GGAGAGAGAGAGAGAGGAGGA 58.591 57.143 0.00 0.00 0.00 3.71
833 963 0.912486 GAGGGAGTGGTGGTGCTTAT 59.088 55.000 0.00 0.00 0.00 1.73
895 1025 4.034258 CCGCTGCTGTTGTGGCTG 62.034 66.667 0.00 0.00 0.00 4.85
898 1028 3.594775 TTGCCGCTGCTGTTGTGG 61.595 61.111 0.70 0.00 38.71 4.17
899 1029 2.353839 GTTGCCGCTGCTGTTGTG 60.354 61.111 0.70 0.00 38.71 3.33
900 1030 1.943116 TTTGTTGCCGCTGCTGTTGT 61.943 50.000 0.70 0.00 38.71 3.32
901 1031 1.226916 TTTGTTGCCGCTGCTGTTG 60.227 52.632 0.70 0.00 38.71 3.33
902 1032 1.226945 GTTTGTTGCCGCTGCTGTT 60.227 52.632 0.70 0.00 38.71 3.16
903 1033 2.412937 GTTTGTTGCCGCTGCTGT 59.587 55.556 0.70 0.00 38.71 4.40
911 1041 3.186909 GTTGAAGAAGGTGTTTGTTGCC 58.813 45.455 0.00 0.00 0.00 4.52
934 1066 0.461548 GTGGTGAGGATGCTGATCGA 59.538 55.000 0.00 0.00 0.00 3.59
935 1067 0.531532 GGTGGTGAGGATGCTGATCG 60.532 60.000 0.00 0.00 0.00 3.69
936 1068 0.835941 AGGTGGTGAGGATGCTGATC 59.164 55.000 0.00 0.00 0.00 2.92
937 1069 1.211457 GAAGGTGGTGAGGATGCTGAT 59.789 52.381 0.00 0.00 0.00 2.90
1012 1159 2.672098 GGAGAAGAGGCTGTCCATAGA 58.328 52.381 0.00 0.00 33.74 1.98
1038 1194 3.345808 CCGTTCACCCACACGCAG 61.346 66.667 0.00 0.00 34.98 5.18
1161 1317 3.123620 GTGCGCTTCTGCCAGAGG 61.124 66.667 9.73 0.00 35.36 3.69
1515 1689 0.240145 CGGACTTGTACTCGCTGACA 59.760 55.000 0.00 0.00 0.00 3.58
1765 1939 1.443407 CGAGGTTGCCGAGGATGAT 59.557 57.895 0.00 0.00 0.00 2.45
1911 2085 1.052124 TCTTGGTGAACCGGGACACT 61.052 55.000 24.68 0.00 39.43 3.55
2295 2470 2.547990 AGGGGATTTGGTTAGTCGTCT 58.452 47.619 0.00 0.00 0.00 4.18
2354 2544 9.001542 TCTCACTCTTACTCTTACTCTTACAAC 57.998 37.037 0.00 0.00 0.00 3.32
2371 2561 3.820467 CACTCACTCACTCTCTCACTCTT 59.180 47.826 0.00 0.00 0.00 2.85
2375 2565 3.058293 CACTCACTCACTCACTCTCTCAC 60.058 52.174 0.00 0.00 0.00 3.51
2376 2566 3.145286 CACTCACTCACTCACTCTCTCA 58.855 50.000 0.00 0.00 0.00 3.27
2436 2631 8.337739 AGTATATCCTCCTACCCTTACATACTG 58.662 40.741 0.00 0.00 0.00 2.74
2437 2632 8.479601 AGTATATCCTCCTACCCTTACATACT 57.520 38.462 0.00 0.00 0.00 2.12
2438 2633 9.625747 GTAGTATATCCTCCTACCCTTACATAC 57.374 40.741 0.00 0.00 0.00 2.39
2439 2634 9.355378 TGTAGTATATCCTCCTACCCTTACATA 57.645 37.037 0.00 0.00 32.01 2.29
2440 2635 8.240881 TGTAGTATATCCTCCTACCCTTACAT 57.759 38.462 0.00 0.00 32.01 2.29
2654 2856 9.092876 CACAAAAGGCAGTAAAGTAAAAATTGA 57.907 29.630 0.00 0.00 0.00 2.57
2688 2890 3.837731 TGGTCATGTGTATTCACTGAGGA 59.162 43.478 4.01 0.00 44.14 3.71
2701 2903 7.964559 CAGATTACTAACAACATTGGTCATGTG 59.035 37.037 0.00 0.00 46.23 3.21
2724 2926 4.613925 ATTGTGAGACAAGAAGAGCAGA 57.386 40.909 0.00 0.00 41.94 4.26
2725 2927 5.686159 AAATTGTGAGACAAGAAGAGCAG 57.314 39.130 0.00 0.00 41.94 4.24
2835 3126 3.137176 AGAGAGGGAGAGACTGAGATCTG 59.863 52.174 0.00 0.00 0.00 2.90
2851 3142 5.072058 TGCTACTAGTAACCCTAGAGAGAGG 59.928 48.000 3.76 0.00 45.21 3.69
2887 3203 2.160205 GCTTCCCCAGTAAGTGGTTTC 58.840 52.381 0.00 0.00 46.37 2.78
2901 3222 0.036294 GGACACCACTACTGCTTCCC 60.036 60.000 0.00 0.00 0.00 3.97
3048 3372 2.274760 GGAGCCAGCCAGAGCAAT 59.725 61.111 0.00 0.00 43.56 3.56
3053 3377 3.324930 CACCAGGAGCCAGCCAGA 61.325 66.667 0.00 0.00 0.00 3.86
3056 3380 4.792804 GAGCACCAGGAGCCAGCC 62.793 72.222 5.06 0.00 0.00 4.85
3057 3381 3.715097 AGAGCACCAGGAGCCAGC 61.715 66.667 5.06 0.00 0.00 4.85
3058 3382 2.268280 CAGAGCACCAGGAGCCAG 59.732 66.667 5.06 0.00 0.00 4.85
3059 3383 3.324930 CCAGAGCACCAGGAGCCA 61.325 66.667 5.06 0.00 0.00 4.75
3060 3384 4.106925 CCCAGAGCACCAGGAGCC 62.107 72.222 5.06 0.00 0.00 4.70
3061 3385 2.533974 CTTCCCAGAGCACCAGGAGC 62.534 65.000 0.00 0.00 0.00 4.70
3115 3448 0.687354 GAAGGAAGCAGGGTGAGTGA 59.313 55.000 0.00 0.00 0.00 3.41
3118 3451 1.747709 CATGAAGGAAGCAGGGTGAG 58.252 55.000 0.00 0.00 0.00 3.51
3128 3461 3.963733 CTGGTGGAGCATGAAGGAA 57.036 52.632 0.00 0.00 0.00 3.36
3173 3508 4.043100 GCCACCCCTACCACCACC 62.043 72.222 0.00 0.00 0.00 4.61
3174 3509 4.043100 GGCCACCCCTACCACCAC 62.043 72.222 0.00 0.00 0.00 4.16
3214 3549 4.810345 AGTGATTGACTTTGGGGGTTAAA 58.190 39.130 0.00 0.00 0.00 1.52


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.